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The first chromosome‐level genome for a marine mammal as a resource to study ecology and evolution
Guangyi Fan1,2,3; Yaolei Zhang1,4; Xiaochuan Liu1; Jiahao Wang1; Zeguo Sun1,5; Shuai Sun1; He Zhang1; Jianwei Chen1; Meiqi Lv1; Kai Han1; Xiaoxuan Tan1; Jie Hu1; Rui Guan1; Yuanyuan Fu1; Shanshan Liu1; Xi Chen6; Qiwu Xu1; Yating Qin1; Longqi Liu2; Jie Bai2; Ou Wang2; Jingbo Tang2,7; Haorong Lu5; Zhouchun Shang2; Bo Wang5; Guohai Hu5; Xia Zhao5,7; Yan Zou2; Ao Chen2; Meihua Gong2; Wenwei Zhang2; Simon M.‐Y. Lee3; Songhai Li8; Junnian Liu1; Zhen Li9; Yishan Lu10; Jamal S. M. Sabir11; Mumdooh J. Sabir11; Muhummadh Khan11; Nahid H. Hajrah11; Ye Yin2,12; Karsten Kristiansen12; Huanming Yang2,13; Jian Wang2,13; Xun Xu1,2,5; Xin Liu1,2,5

Marine mammals are important models for studying convergent evolution and aquatic adaption, and thus reference genomes of marine mammals can provide evolutionary insights. Here, we present the first chromosome-level marine mammal genome assembly based on the data generated by the BGISEQ-500 platform, for a stranded female sperm whale (Physeter macrocephalus). Using this reference genome, we performed chromosome evolution analysis of the sperm whale, including constructing ancestral chromosomes, identifying chromosome rearrangement events and comparing with cattle chromosomes, which provides a resource for exploring marine mammal adaptation and speciation. We detected a high proportion of long interspersed nuclear elements and expanded gene families, and contraction of major histocompatibility complex region genes which were specific to sperm whale. Using comparisons with sheep and cattle, we analysed positively selected genes to identify gene pathways that may be related to adaptation to the marine environment. Further, we identified possible convergent evolution in aquatic mammals by testing for positively selected genes across three orders of marine mammals. In addition, we used publicly available resequencing data to confirm a rapid decline in global population size in the Pliocene to Pleistocene transition. This study sheds light on the chromosome evolution and genetic mechanisms underpinning sperm whale adaptations, providing valuable resources for future comparative genomics.

KeywordAncestral Chromosomes Aquatic Adaptations Genome Assembly Genomics/proteomics Major Histocompatibility Complex Mammals Molecular Evolution Sperm Whale
Indexed BySCIE
WOS Research AreaBiochemistry & Molecular Biology ; Environmental Sciences & Ecology ; Evolutionary Biology
WOS SubjectBiochemistry & Molecular Biology ; Ecology ; Evolutionary Biology
WOS IDWOS:000471830200011
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Cited Times [WOS]:12   [WOS Record]     [Related Records in WOS]
Document TypeJournal article
CollectionUniversity of Macau
Corresponding AuthorXin Liu
Affiliation1.BGI-Qingdao, BGI-Shenzhen, Qingdao, Shandong Province, China
2.BGI-Shenzhen, Shenzhen, China
3.State Key Laboratory of Quality Research of Chinese Medicine and Institute of Chinese Medical Sciences, University of Macau, Macau, China
4.Department of Biotechnology and Biomedicine, Technical University of Denmark, Lyngby, Denmark
5.China National GeneBank, BGI‐Shenzhen, Shenzhen, China
6.Guangdong Pearl River Estuary Chinese White Dolphin National Nature Reserve Administration, Zhu Hai, Guangdong, China
7.MGI, BGI‐Shenzhen, Shenzhen, China
8.Marine Mammal and Marine Bioacoustics Laboratory, Institute of Deep‐Sea Science and Engineering, Chinese Academy of Science, Sanya, China
9.Health and Family Planning Integrated Supervision Enforcement Bureau of Shinan District, Qingdao City, China
10.Guangdong Ocean University, Shenzhen, China
11.Department of Biological Sciences, King Abdulaziz University (KAU), Jeddah, Saudi Arabia
12.Department of Biology, University of Copenhagen, Copenhagen, Denmark
13.James D. Watson Institute of Genome Sciences, Hangzhou, China
First Author AffilicationInstitute of Chinese Medical Sciences
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GB/T 7714
Guangyi Fan,Yaolei Zhang,Xiaochuan Liu,et al. The first chromosome‐level genome for a marine mammal as a resource to study ecology and evolution[J]. MOLECULAR ECOLOGY RESOURCES,2019,19(4):944-956.
APA Guangyi Fan.,Yaolei Zhang.,Xiaochuan Liu.,Jiahao Wang.,Zeguo Sun.,Shuai Sun.,He Zhang.,Jianwei Chen.,Meiqi Lv.,Kai Han.,Xiaoxuan Tan.,Jie Hu.,Rui Guan.,Yuanyuan Fu.,Shanshan Liu.,Xi Chen.,Qiwu Xu.,Yating Qin.,Longqi Liu.,...&Xin Liu.(2019).The first chromosome‐level genome for a marine mammal as a resource to study ecology and evolution.MOLECULAR ECOLOGY RESOURCES,19(4),944-956.
MLA Guangyi Fan,et al."The first chromosome‐level genome for a marine mammal as a resource to study ecology and evolution".MOLECULAR ECOLOGY RESOURCES 19.4(2019):944-956.
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